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Pubmed for Handhelds

PUBMED FOR HANDHELDS

Journal Abstract Search

210 related items for PubMed ID: 30053414

  • 21. MONALISA for stochastic simulations of Petri net models of biochemical systems.
    Balazki P, Lindauer K, Einloft J, Ackermann J, Koch I.
    BMC Bioinformatics; 2015 Jul 10; 16():215. PubMed ID: 26156221
    [Abstract] [Full Text] [Related]

  • 22. SBMLToolbox: an SBML toolbox for MATLAB users.
    Keating SM, Bornstein BJ, Finney A, Hucka M.
    Bioinformatics; 2006 May 15; 22(10):1275-7. PubMed ID: 16574696
    [Abstract] [Full Text] [Related]

  • 23. Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models.
    Matzko RO, Mierla L, Konur S.
    Genes (Basel); 2023 Jan 06; 14(1):. PubMed ID: 36672895
    [Abstract] [Full Text] [Related]

  • 24. NeuroPycon: An open-source python toolbox for fast multi-modal and reproducible brain connectivity pipelines.
    Meunier D, Pascarella A, Altukhov D, Jas M, Combrisson E, Lajnef T, Bertrand-Dubois D, Hadid V, Alamian G, Alves J, Barlaam F, Saive AL, Dehgan A, Jerbi K.
    Neuroimage; 2020 Oct 01; 219():117020. PubMed ID: 32522662
    [Abstract] [Full Text] [Related]

  • 25. SBML Level 3: an extensible format for the exchange and reuse of biological models.
    Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Level 3 Community members.
    Mol Syst Biol; 2020 Aug 01; 16(8):e9110. PubMed ID: 32845085
    [Abstract] [Full Text] [Related]

  • 26. Supporting SBML as a model exchange format in software applications.
    Keating SM, Le Novère N.
    Methods Mol Biol; 2013 Aug 01; 1021():201-25. PubMed ID: 23715987
    [Abstract] [Full Text] [Related]

  • 27. SBML export interface for the systems biology toolbox for MATLAB.
    Schmidt H, Drews G, Vera J, Wolkenhauer O.
    Bioinformatics; 2007 May 15; 23(10):1297-8. PubMed ID: 17384017
    [Abstract] [Full Text] [Related]

  • 28. SBtab: a flexible table format for data exchange in systems biology.
    Lubitz T, Hahn J, Bergmann FT, Noor E, Klipp E, Liebermeister W.
    Bioinformatics; 2016 Aug 15; 32(16):2559-61. PubMed ID: 27153616
    [Abstract] [Full Text] [Related]

  • 29. Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python.
    Lubbock ALR, Lopez CF.
    Bioinformatics; 2022 Oct 14; 38(20):4823-4825. PubMed ID: 36000837
    [Abstract] [Full Text] [Related]

  • 30. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.
    Stoma S, Fröhlich M, Gerber S, Klipp E.
    BMC Bioinformatics; 2011 Apr 28; 12():126. PubMed ID: 21527030
    [Abstract] [Full Text] [Related]

  • 31. sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology.
    Scott-Brown J, Papachristodoulou A.
    ACS Synth Biol; 2017 Jul 21; 6(7):1225-1229. PubMed ID: 28035814
    [Abstract] [Full Text] [Related]

  • 32. SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
    Zi Z, Zheng Y, Rundell AE, Klipp E.
    BMC Bioinformatics; 2008 Aug 15; 9():342. PubMed ID: 18706080
    [Abstract] [Full Text] [Related]

  • 33. MakeSBML: a tool for converting between Antimony and SBML.
    Jardine BE, Smith LP, Sauro HM.
    J Integr Bioinform; 2024 Mar 01; 21(1):. PubMed ID: 38860571
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  • 34. Computational modeling of biochemical networks using COPASI.
    Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U.
    Methods Mol Biol; 2009 Mar 01; 500():17-59. PubMed ID: 19399433
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  • 35. JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
    Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.
    Bioinformatics; 2015 Oct 15; 31(20):3383-6. PubMed ID: 26079347
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  • 36. Python interfaces for the Smoldyn simulator.
    Singh D, Andrews SS.
    Bioinformatics; 2021 Dec 22; 38(1):291-293. PubMed ID: 34293100
    [Abstract] [Full Text] [Related]

  • 37. General, open-source vertex modeling in biological applications using Tissue Forge.
    Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA.
    Sci Rep; 2023 Oct 19; 13(1):17886. PubMed ID: 37857673
    [Abstract] [Full Text] [Related]

  • 38. Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.
    Yu SH, Ferretti D, Schessner JP, Rudolph JD, Borner GHH, Cox J.
    Curr Protoc Bioinformatics; 2020 Sep 19; 71(1):e105. PubMed ID: 32931150
    [Abstract] [Full Text] [Related]

  • 39. GPU accelerated biochemical network simulation.
    Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.
    Bioinformatics; 2011 Mar 15; 27(6):874-6. PubMed ID: 21224286
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  • 40. MOCCASIN: converting MATLAB ODE models to SBML.
    Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.
    Bioinformatics; 2016 Jun 15; 32(12):1905-6. PubMed ID: 26861819
    [Abstract] [Full Text] [Related]

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